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(-) Description

Title :  CRYSTAL STRUCTURE OF A SUGAR PHOSPHATE ISOMERASE/EPIMERASE (BDI_3400) FROM PARABACTEROIDES DISTASONIS ATCC 8503 AT 1.70 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  06 Aug 10  (Deposition) - 01 Sep 10  (Release) - 20 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-Biology, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of A Sugar Phosphate Isomerase/Epimerase (Bdi_3400) From Parabacteroides Distasonis Atcc 8503 At 1. 7 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SUGAR PHOSPHATE ISOMERASE/EPIMERASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BDI_3400
    Organism Scientific: PARABACTEROIDES DISTASONIS
    Organism Taxid: 435591
    Strain: ATCC 8503

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 32)

Asymmetric Unit (3, 32)
No.NameCountTypeFull Name
1EOH10Ligand/IonETHANOL
2MSE20Mod. Amino AcidSELENOMETHIONINE
3PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 16)
No.NameCountTypeFull Name
1EOH5Ligand/IonETHANOL
2MSE10Mod. Amino AcidSELENOMETHIONINE
3PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (3, 16)
No.NameCountTypeFull Name
1EOH5Ligand/IonETHANOL
2MSE10Mod. Amino AcidSELENOMETHIONINE
3PO41Ligand/IonPHOSPHATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:53 , HIS A:121 , HIS A:194 , HIS A:196 , GLU A:302 , EOH A:407 , HOH A:418 , HOH A:682 , HOH A:684BINDING SITE FOR RESIDUE PO4 A 400
02AC2SOFTWAREGLY A:49 , ASP A:77 , GLY A:298 , TYR A:299 , TYR A:300 , HOH A:900BINDING SITE FOR RESIDUE EOH A 402
03AC3SOFTWAREARG A:116 , SER A:154 , HOH A:857BINDING SITE FOR RESIDUE EOH A 403
04AC4SOFTWARETYR A:53BINDING SITE FOR RESIDUE EOH A 405
05AC5SOFTWARELEU A:60 , PHE A:81 , TYR A:106BINDING SITE FOR RESIDUE EOH A 406
06AC6SOFTWAREGLN A:51 , TYR A:53 , HIS A:121 , PRO A:159 , PO4 A:400 , HOH A:705BINDING SITE FOR RESIDUE EOH A 407
07AC7SOFTWAREHIS B:121 , HIS B:194 , HIS B:196 , GLU B:302 , EOH B:408 , HOH B:445 , HOH B:612 , HOH B:841BINDING SITE FOR RESIDUE PO4 B 401
08AC8SOFTWARELYS B:47 , GLY B:49 , ASP B:77 , GLY B:298 , TYR B:299BINDING SITE FOR RESIDUE EOH B 404
09AC9SOFTWAREGLN B:51 , TYR B:53 , TYR B:93 , HIS B:121 , PRO B:159 , PO4 B:401 , HOH B:961BINDING SITE FOR RESIDUE EOH B 408
10BC1SOFTWAREARG B:116 , SER B:154 , TYR B:300BINDING SITE FOR RESIDUE EOH B 409
11BC2SOFTWARELEU B:60 , PHE B:81 , TYR B:106BINDING SITE FOR RESIDUE EOH B 410
12BC3SOFTWARELYS A:171 , LYS A:308 , GLU B:256 , ASN B:260 , HOH B:852BINDING SITE FOR RESIDUE EOH B 411

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OBE)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3OBE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OBE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3OBE)

(-) Exons   (0, 0)

(no "Exon" information available for 3OBE)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:286
 aligned with A6LHD8_PARD8 | A6LHD8 from UniProtKB/TrEMBL  Length:330

    Alignment length:298
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322        
         A6LHD8_PARD8    33 IPATDAVSSATAGKKMGLQTYSLGQELLQDMPNGLNRLAKAGYTDLEIFGYREDTGKFGDYNPKNTTFIASKDYKKMVDDAGLRISSSHLTPSLREYTKENMPKFDEFWKKATDIHAELGVSCMVQPSLPRIENEDDAKVVSEIFNRAGEITKKAGILWGYHNHSNEFKRVLKAGEKPEQNPNPWAPPKGTYIEELFLKNTDPDKVMFELDVYWAVMGQQDPVEWMENYPNRFKLLHIKDRWIIGDSGMMNFPNIFKKAYEIGILGYYVELEGDKKGRTQFEGVEKSAAYLQAAPFVK 330
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eee.hhhhhhhhhhhhhhhhhhhhhh..eeee.............----....hhhhhhhhhhhh..eeeee.........hhhhhhhhhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhhhhhhh...eeeee..hhhh.ee........--------...eehhhhhhhhh....eeeeeehhhhhhh..hhhhhhhhh...eeeeee............hhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3obe A  33 IPATDAVSSATAGKKmGLQTYSLGQELLQDmPNGLNRLAKAGYTDLEIFGYREDTGKFGDY----TTFIASKDYKKmVDDAGLRISSSHLTPSLREYTKENmPKFDEFWKKATDIHAELGVSCmVQPSLPRIENEDDAKVVSEIFNRAGEITKKAGILWGYHNHSNEFKRVLKAGEKPE--------PKGTYIEELFLKNTDPDKVmFELDVYWAVmGQQDPVEWmENYPNRFKLLHIKDRWIIGDSGmmNFPNIFKKAYEIGILGYYVELEGDKKGRTQFEGVEKSAAYLQAAPFVK 330
                                    42     |  52        62|       72        82        92|    | 102      |112       122       132 |     142       152   |   162       172       182       192       202        |-       222       232      |242      |252     | 262       272       282       292       302       312       322        
                                          48-MSE         63-MSE                        93   98        109-MSE                  134-MSE               156-MSE                                                211      220                239-MSE   249-MSE  258-MSE                281-MSE                                             
                                                                                                                                                                                                                                                                                   282-MSE                                            


Chain B from PDB  Type:PROTEIN  Length:290
 aligned with A6LHD8_PARD8 | A6LHD8 from UniProtKB/TrEMBL  Length:330

    Alignment length:292
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328  
         A6LHD8_PARD8    39 VSSATAGKKMGLQTYSLGQELLQDMPNGLNRLAKAGYTDLEIFGYREDTGKFGDYNPKNTTFIASKDYKKMVDDAGLRISSSHLTPSLREYTKENMPKFDEFWKKATDIHAELGVSCMVQPSLPRIENEDDAKVVSEIFNRAGEITKKAGILWGYHNHSNEFKRVLKAGEKPEQNPNPWAPPKGTYIEELFLKNTDPDKVMFELDVYWAVMGQQDPVEWMENYPNRFKLLHIKDRWIIGDSGMMNFPNIFKKAYEIGILGYYVELEGDKKGRTQFEGVEKSAAYLQAAPFVK 330
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------AP_endonuc_2-3obeB01 B:67-28  4                                                                                                                                                                                           ---------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----------------------------AP_endonuc_2-3obeB02 B:67-28  4                                                                                                                                                                                           ---------------------------------------------- Pfam domains (2)
         Sec.struct. author ..........eee.hhhhhhhhhhhhhhhhhhhhh...eeee..............--.....hhhhhhhhhhhh..eeeee.........hhhhhhhhhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhhhhhhh...eeeee..hhhh.ee...................eehhhhhhhhh....eeeeeehhhhhhh..hhhhhhhhh...eeeeee............hhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3obe B  39 VSSATAGKKmGLQTYSLGQELLQDmPNGLNRLAKAGYTDLEIFGYREDTGKFGDYN--NTTFIASKDYKKmVDDAGLRISSSHLTPSLREYTKENmPKFDEFWKKATDIHAELGVSCmVQPSLPRIENEDDAKVVSEIFNRAGEITKKAGILWGYHNHSNEFKRVLKAGEKPEQNPNPWAPPKGTYIEELFLKNTDPDKVmFELDVYWAVmGQQDPVEWmENYPNRFKLLHIKDRWIIGDSGmmNFPNIFKKAYEIGILGYYVELEGDKKGRTQFEGVEKSAAYLQAAPFVK 330
                                    48        58    |   68        78        88     |  98       108|      118       128     | 138       148       158       168       178       188       198       208       218       228       238|      248|      258       268       278  ||   288       298       308       318       328  
                                    48-MSE         63-MSE                         94 97         109-MSE                  134-MSE               156-MSE                                                                            239-MSE   249-MSE  258-MSE                281-MSE                                             
                                                                                                                                                                                                                                                                             282-MSE
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3OBE)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OBE)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (A6LHD8_PARD8 | A6LHD8)
molecular function
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.

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